title: Multiscale spatial organization of RNA polymerase in Escherichia coli.
abstract: Nucleic acid synthesis is spatially organized in many organisms. In bacteria, however, the spatial distribution of transcription remains obscure, owing largely to the diffraction limit of conventional light microscopy (200-300 nm). Here, we use photoactivated localization microscopy to localize individual molecules of RNA polymerase (RNAP) in Escherichia coli with a spatial resolution of ∼40 nm. In cells growing rapidly in nutrient-rich media, we find that RNAP is organized in 2-8 bands. The band number scaled directly with cell size (and so with the chromosome number), and bands often contained clusters of >70 tightly packed RNAPs (possibly engaged on one long ribosomal RNA operon of 6000 bp) and clusters of such clusters (perhaps reflecting a structure like the eukaryotic nucleolus where many different ribosomal RNA operons are transcribed). In nutrient-poor media, RNAPs were located in only 1-2 bands; within these bands, a disproportionate number of RNAPs were found in clusters containing ∼20-50 RNAPs. Apart from their importance for bacterial transcription, our studies pave the way for molecular-level analysis of several cellular processes at the nanometer scale.
authors.affiliation: Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Endesfelder
authors.forename: Kieran
authors.initials: K
authors.lastname: Finan
authors.forename: Seamus J
authors.initials: SJ
authors.lastname: Holden
authors.forename: Peter R
authors.initials: PR
authors.lastname: Cook
authors.forename: Achillefs N
authors.initials: AN
authors.lastname: Kapanidis
authors.forename: Mike
authors.initials: M
authors.lastname: Heilemann
mesh_terms: D004247:DNA / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli / Q000166:cytology / Q000201:enzymology*; D008853:Microscopy; D057054:Molecular Imaging; D049329:Nanostructures / Q000737:chemistry; D009876:Operon / Q000235:genetics; D021381:Protein Transport; D012335:RNA, Ribosomal / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D012335:RNA, Ribosomal; D004247:DNA; D012321:DNA-Directed RNA Polymerases